In one of my current projects I have a character known as "Cipher". In short: Cipher lives in a world with three factions. The Reavers (Evil), Nobles ("Good"), and the Judges ("Neutral").

Now in reality this is a triumvirate, three factions lead by supreme beings battling it out for supremacy. Cipher is apart of the Judge Faction, who's goal is to appear to remain neutral, but to secretly continue the war between the Reavers and Nobles in order to weaken both sides so that they will be able to spring and defeat them both.

Cipher, with no relations to his Family and has little to no friends, works for his faction as a Operative. He's essentially the James Bond protagonist without the accent. Now, my dilemma is the way readers will take Cipher. I want to display him as a good man at heart, but yet he commits sinister deeds and is a master at manipulation.

I'm concerned that Readers will take Cipher as a Villain for deceiving both factions to gain power for his own. When I don't want the Reader to take Cipher as the Harry Potter and Superman character of justice, doing the best deeds possible and showing restraint. When his job calls for murder, deception, and espionage. So I feel that Cipher fits neither the Hero or Villain. It almost reminds me of the Count of Monte Christo. Where the Protagonist is a hero in his own right for seeking revenge (As it is apart of the Hero Cycle) and a Villain for extracting the revenge with such malice.

His character is almost conflicting with everything he stands for and I'm not sure how to progress from there. Does anybody know a term that would describe Cipher? Or a Character from another Novel/Movie that might match his intentions and positions?

TV Tropes, if you're not already familiar with the site, has a whole list of tropes and examples on almost every aspect of storytelling.

Looking up Anti-Hero is a good place to start, but Anti-Villain is another similar character trope from the opposite side that seems a bit more descriptive of your character. Anti-Villains are generally characters who do evil actions although they are good at heart, and they can easily wind up being reader favorites.

In truth, the best characters are neither hero nor villain. They're merely human.

Look at it this way. What does Cipher want? Why does he want what he does? Why does he do these things? If you show those, you're good to go. There are terrible people, yes, but even they have their reasons. If you saw it from his point of view, you wouldn't think he was evil. You'd think he was misunderstood, and you'd understand that if you were in his footsteps then there wouldn't have been anything else to do. Or, if there was something else he could do, you'd feel as though you know why he did it.

Motive is the biggest factor in the whole thing. If the audience understands the character's motives and the reasons beneath the motive, then they won't dislike a character as much.

For examples, check Kyll's links. I'd particularly recommend Code Geass and Death Note for examples of ruthless protagonists with their hearts in the right places. As for books, that's a bit trickier. Artemis Fowl is one, I suppose, although not too much so. He's certainly morally ambiguous, though. I think the best examples of moral ambiguity so far has to be the entire cast of A Song of Ice and Fire, though. It's an excellent series, but the first book is enough if you want to have a feel for a world without a true hero or villain.

"The moral of this story, is that if I cause a stranger to choke to death for my amusement, what do you think I’ll do to you if you don’t tell me who ordered you to kill Colosimo?“

Your character is known as a good/bad guy. Characters like this are my favorite. Take Guy of Gisborne from the TV series Robin Hood. Guy is amazing, Robin the hero is well....yeah...and The Sheriff is just the bad guy neither of which I like. But Guy has more conflict, more depth, and is just a better character.

Stop worrying about what others will think, its impossible to please everyone, plus it just wears you out. Follow your fingers and let your character do what he needs to do. Why micromanage? It stifles the story.

"Me I'm dishonest but a dishonest man you can always trust to be dishonest. Honestly its the honest ones you have to watch out for because you can never tell when they are going to do something incredibly...stupid." ~Capt. Jack Sparrow